Connections are prime spot for heat build up. Especially if there is any corrosion. I would check and clean every connection from the trolling motor to the battery. Even slightly loose connections can start to arc leading to more heat buildup.
Some questions
1) what size and voltage is Trolling motor? ie 12, 24 or 36 volt? lbs of thrust 30, 55, 80, 112?
2) How high was trolling motor set to run. just putting along or as fast as would go? Fast means more current draw, and more heat.
3) How long of a run from trolling motor to switch 6 ga wire, switch to battery 4 ga?
4) How long is orginal wire from trolling motor to 6ga wire and how are they connected?
For my 12V 55 thrust motor it came with about 6 ft of 10 ga wire. I melted one trolling motor plug and connector by running at top speed for about 20 minutes to get to where I wanted to fish(electric only lake). When I rewired this winter I cut the 10 ga down to 18 inches and used a high quality connector to connect to 4 ga running to the breaker and battery.
This is what I used, but I had access to tools to be able to crimp them correctly. They are rated for 120amps max and can be disconnected while carrying up to 50 amps. I only unplug when trolling motor is turned off so there is zero of very little current in the circuit.
https://powerwerx.com/anderson-sb-connectors-sb50-50amp
There are other types and styles out there that you shouldn't need special tool to make use of.
Wire chart for suggested amps and gauge based on length of circuit
https://www.westmarine.com/WestAdvisor/Marine-Wire-Size-And-Ampacity